Search – Common Metabolic Diseases Genome Atlas

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Publication
released
Systematic Functional Characterization of Candidate Causal Genes for Type 2 Diabetes Risk Variants
Thomsen SK, Ceroni A, van de Bunt M, et al.
December 2016;(65(12)):3805-3811.
- PMID:27554474
- doi:10.2337/db16-0361
Publication
released
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
Kevin W Currin, Hannah J Perrin, Gautam K Pandey, et al.
Genome Res. 2025-05-20;
- doi:10.1101/gr.279741.124
- PMID:40393811
Publication
released
A comprehensive spatio-cellular map of the human hypothalamus
John A. Tadross, Lukas Steuernagel, Georgina K. C. Dowsett, et al.
Nature. 2025-02-05;639(8055):708-716.
URL: https://www.nature.com/articles/s41586-024-08504-8
Publication
released
Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2
Sheridan H Littleton, Khanh B Trang, Christina M Volpe, et al.
Cell Genomics. 2024-05-08;
Data summary: Hi-C, RNA-seq, ATAC-seq, single-nucleus RNA-seq, and single-nucleus ATAC-seq data have been…
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241592
Data summary: Raw and processed Hi-C data GEO: GSE241592
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241050
Data summary: Raw and processed RNA-seq data GEO: GSE241050
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241591
Data summary: Raw and processed ATAC-seq data GEO: GSE241591
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241594
Data summary: Raw and processed single-nucleus RNA-seq data GEO: GSE241594
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241593
Data summary: Raw and processed single-nucleus ATAC-seq data GEO: GSE241593;
Publication
released
Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes
Norbert Bittner, Chenfu Shi, Danyun Zhao, et al.
Ann Rheum Dis. 2024-03-13;:ard-2023-224945.
- PMID:38479789
- doi:10.1136/ard-2023-224945
Publication
released
An integrated map of cell type-specific gene expression in pancreatic islets
Ruth M Elgamal, Parul Kudtarkar, Rebecca L Melton, et al.
Diabetes. 2023-15-08;(db230130)
- PMID:37582230
- doi:10.2337/db23-0130
Publication
released
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation
Arushi Varshney Arushi Varshney, Nandini Manickam, Peter Orchard, et al.
bioRxiv. 2023-12-15;
URL: https://www.biorxiv.org/content/10.1101/2023.12.15.571696v2
Publication
released
Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits
Sarah M Brotman, Anniina Oravilahti, Jonathan D Rosen, et al.
Diabetes. 2023-11-01;72(11):1707-1718.
Publication
released
A comparative atlas of single-cell chromatin accessibility in the human brain
Yang Eric Li, Sebastian Preissl, Michael Miller, et al.
Science. 2023-10-13;382(6667)
Publication
released
An atlas of healthy and injured cell states and niches in the human kidney
Blue B. Lake, Rajasree Menon, Seth Winfree, et al.
Nature. 2023-07-19;619(7970):585-594.
URL: https://www.nature.com/articles/s41586-023-05769-3
Publication
released
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes
Kristina M. Garske, Asha Kar, Caroline Comenho, et al.
Nat Commun. 2023-07-14;14(1):4214.
Publication
released
Lineage-specific differences and regulatory networks governing human chondrocyte development
Daniel Richard, Steven Pregizer, Divya Venkatasubramanian, et al.
Elife. 2023-03-15;15:12:e79925
Publication
released
Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression
Katia K. Mattis, Nicole A. J. Krentz, Christoph Metzendorf, et al.
Diabetologia. 2023-01-12;
- doi:10.1007/s00125-022-05856-6
- PMID:36633628
Publication
released
Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
Paola Benaglio, Han Zhu, Mei-Lin Okino, et al.
Cell Genomics. 2022-12-14;2(12):100214.
Publication
released
Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis
Kristina M Garske, Caroline Comenho, David Z Pan, et al.
Epigenetics. 2022-12-01;17(13):1849-1862.
Available supplemental data: website
File format: other format
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129574
Data summary: Assay for transposase accessible chromatin (ATAC) -seq libraries were produced from human primary…
Publication
released
Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk
Ricardo D’Oliveira Albanus, Xuming Tang, Henry J. Taylor, et al.
bioRxiv. 2022-11-14;
- doi:10.1101/2022.11.12.516291
Publication
released
Genetic regulation of RNA splicing in human pancreatic islets
Goutham Atla, Silvia Bonàs-Guarch, Mirabai Cuenca-Ardura, et al.
Genome Biol. 2022-09-15;23(1):196.
URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02757-0#Sec36
Available supplemental data: website
File format: text
URL: https://zenodo.org/record/6546807#.Y-wbZi-B39B
Publication
released
Characterizing cis-regulatory elements using single-cell epigenomics
Sebastian Preissl, Kyle J Gaulton, Bing Ren.
Nat Rev Genet. 2022-07-15;
- doi:10.1038/s41576-022-00509-1
- PMID:35840754
Publication
released
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease
Hongbo Liu, Tomohito Doke, Dong Guo, et al.
Nature Genetics. 2022-06-16;54:950–962.
- PMID:35710981
- doi:10.1038/s41588-022-01097-w
Available supplemental data: website
URL: https://github.com/hbliu/Kidney_Epi_Pri
Data summary: Customized code used in the present study is available at github
Available supplemental data: website
URL: https://doi.org/10.5281/zenodo.6392494
Data summary: Zenodo
Publication
released
Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity
Steven Gazal, Omer Weissbrod, Farhad Hormozdiari, et al.
Nature Genetics. 2022-06-06;(2022)
- doi:10.1101/2021.08.02.21261488
URL: https://doi.org/10.5281/zenodo.6354007
Data summary: The list of 19,995 genes, summary statistics of the 63 independent traits, training and validation…
Data summary: Links for all data sets used to create S2G strategies are provided in Supplementary Table 26.
URL: http://www.ukbiobank.ac.uk/
Data summary: Access to the UK Biobank resource is available via application
URL: https://www.ebi.ac.uk/gwas/api/search/downloads/full
Data summary: The GWAS Catalog is available
URL: https://raw.githubusercontent.com/opentargets/genetics-gold-standards/master/gold_standards/processed/gwas_gold_standards.191108.tsv
Data summary: Open Targets SNP–gene pairs are available
URL: https://www.dropbox.com/s/kz2c49rpm2yanf5/all_byCS_rev1.txt?dl=0
Data summary: SNP–gene pairs from ref48 are available
URL: https://alkesgroup.broadinstitute.org/cS2G/code
Data summary: The code to estimate precision and recall of S2G strategies and the code to create combined S2G…
URL: https://doi.org/10.5281/zenodo.6415925
Data summary: The code to estimate precision and recall of S2G strategies and the code to create combined S2G…
Publication
released
A single-cell atlas of human and mouse white adipose tissue
Margo P. Emont, Christopher Jacobs, Adam L. Essene, et al.
Nature. 2022-03-16;603(7903):926-933.
URL: https://www.nature.com/articles/s41586-022-04518-2
Publication
released
A mechanistic framework for cardiometabolic and coronary artery diseases
Simon Koplev, Marcus Seldin, Katyayani Sukhavasi, et al.
Nat Cardiovasc Res. 2022-01-12;1(1):85-100.
Available supplemental data: website
URL: http://starnet.mssm.edu
Data summary: The website was developed with a Python Flask backend and a sqlite3 database, with an application…
Publication
released
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
Peter Orchard, Nandini Manickam, Christa Ventresca, et al.
Genome Res. 2021-11-23;31(12):2258-2275.
URL: https://zenodo.org/search?page=1&size=20&q=5009200
URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178735
Publication
released
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
Hannah J Perrin, Kevin W Currin, Swarooparani Vadlamudi, et al.
PLoS Genet. 2021-10-26;17(10):e1009865.
Publication
released
TIGER: The gene expression regulatory variation landscape of human pancreatic islets
Lorena Alonso, Anthony Piron, Ignasi Morán, et al.
Cell Rep. 2021-10-12;37(2):109807.
Data summary: RNA-seq and genotyping array data from PISA cohort Sequence data have been deposited at the…

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Showing 25 of 94 results